Identification of novel epigenetic markers for clear cell renal cell carcinoma
Identification of novel epigenetic markers for clear cell renal cell carcinoma
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DOI：
10.1016/j.juro.2008.04.137
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发表时间：
2008-09-01
影响因子：
6.6
通讯作者：
Liou, Louis S.
中科院分区：
文献类型：
--
作者：
Dalgin, Gul S.;Drever, Michele;Liou, Louis S.
目的：我们在透明细胞肾细胞癌中发现了显著的高甲基化基因。材料和方法：我们之前通过转录谱分析和强大的计算筛选在肾细胞癌组织中鉴定了一组表达不足的基因。考虑到CpG岛和转录因子结合位点，通过严格搜索最佳候选区域，我们选择了其中的19个基因进行超甲基化分析。采用基质辅助激光解吸电离飞行时间质谱分析了38例匹配的透明细胞肾细胞癌和正常样本DNA中这些基因的高甲基化。采用3个统计学检验评估高甲基化的显著性。我们使用逆转录聚合酶链反应、免疫组织化学和Western blots验证了在一组单独的患者中RNA和蛋白质水平上显著高甲基化基因的下调。结果：我们在6个下调基因中发现了7个显著的高甲基化区域，其中包括SFRP1，该基因先前被证明在肾细胞癌和其他类型的癌症中高甲基化。结论：据我们所知，我们首次报道了另外5个基因（SCNN1B、SYT6、DACH1以及肿瘤抑制因子TFAP2A和MT1G）在肾细胞癌中高甲基化。强大的计算筛选和高通量甲基化分析导致透明细胞肾细胞癌中丰富的一组新基因发生表观遗传改变。总的来说，在这些高度下调的基因中检测到高甲基化表明，使用尿液或血液细胞检测它们的甲基化可以为可行的诊断测试提供基础。
Purpose: We identified significantly hypermethylated genes in clear cell renal cell carcinoma.Materials and Methods: We previously identified a set of under expressed genes in renal cell carcinoma tissue through transcriptional profiling and a robust computational screen. We selected 19 of these genes for hypermethylation analysis using a rigorous search for the best candidate regions, considering CpG islands and transcription factor binding sites. The genes were analyzed for hypermethylation in the DNA of 38 matched clear cell renal cell carcinoma and normal samples using matrix assisted laser desorption ionization time-of-flight mass spectrometry. The significance of hypermethylation was assessed using 3 statistical tests. We validated the down-regulation of significantly hypermethylated genes at the RNA and protein levels in a separate set of patients using reverse transcriptase-polymerase chain reaction, immunohistochemistry and Western blots.Results: We found 7 significantly hypermethylated regions from 6 down-regulated genes, including SFRP1, which was previously shown to be hypermethylated in renal cell carcinoma and other cancer types.Conclusions: To our knowledge we report for the first time that another 5 genes (SCNN1B, SYT6, DACH1, and the tumor suppressors TFAP2A and MT1G) are hypermethylated in renal cell carcinoma. Robust computational screens and the high throughput methylation assay resulted in an enriched set of novel genes that are epigenetically altered in clear cell renal cell carcinoma. Overall the detection of hypermethylation in these highly down-regulated genes suggests that assaying for their methylation using cells from urine or blood could provide the basis for a viable diagnostic test.